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Created with Raphaël 2.2.04Oct32130Sep27262523191817131211109653230Aug29272322201916151298765231Jul302926252423221918171615111043228Jun27262421201918171312111065331May302928232221171514131098732130Apr2927262423221918171615121110953227Mar26252221201918151211654128Feb27262522212019181514131211754130Jan29252422211716151410987421Dec2019171413Removing now deprecated callsTwo new metazoans (pine beetle and fire ant)[ENSCORESW-577]. Additional lookup would not work if it was the first call.Allow pass_through in GetOpt::Long some circumstances.[ENSCORESW-577]. Fixing a logical hole where we reqiured a method to be defined but did nothing with it.add external_name (display_label) in transcript summary_as_hashfor chromosome Y, we want the whole sequence as one slice, so use 'include duplicates'ENSCORESW-678: added _columns and _tables methodsENSCORESW-678: added special case for density featurecorrect typoremoving smart match operators from the test suite[ENSCORESW-691]. Adding the ability to query by retired seq region ids.Fixed a warning that was testing the wrong value and failing to verify a store_alt_alleles call properlyRemove qtl_feature table. It doesn't exist any more.[ENSCORESW-665]. Making sure we report the correct DBI error.[ENSCORESW-680]. Adding a max allowed time limit to optimise a tree in for web.[ENSCORESW-680]. Adding a max allowed time limit to optimise a tree in for web.[ENSCORESW-689]. Allowing more IDs when querying for a list of dbIDs as integers.Found more deprecated callsFixes for the alt alleles code. We needed to make sure we used the right variables in the code. Also needed to make sure an array is actually defined during constructionFixing an issue raised by vega and non-standard DBAdaptor group names. Vega use ensembl to denote the ensembl db. We assumed incorrectly that core could always be used. That would always fail the moment a different group name was usedSpecify memory requirements for dependent job [farm3].removed the deprecated callDeprecating a number of calls. Instead we want more API compatible callsMaking this script new alt allele compatibleadded test for fetch_all_by_feature_class methodAdd the missing configuration options for the production database.Add memory resources to job waiting for exonerate to finish. RequiredFarm3 seems to require memory resources on the job that waits on theUpdated for farm3 (unit for bsub's -M switch was changed for new farm).Making consistent through plants species the use of ncRNA_EG source for maintaining ncRNA genes xrefs asscoiated with logic_name ncrna_egadded species-specific refseq_dna and refseq_peptide sources where availableENSCORESW-660: added ChEMBL source as part of the Uniprot dependent xrefsENSCORESW-660: when looking for EMBL, make sure it is not ChEMBLadded more methods:ENSCORESW-677: test updated to include get_all_versions methodENSCORESW-677: added method get_all_versionsCCDS db (human, mouse) updated to 74Ontology db updated to 74ENSCORESW-677: added test for get_default_version method